Why does the United States government give patents to pharmeceutical companies? Specifically?

Can anyone explain how patents and copyrights differ in the protections they offer to software source code. In what ways a software company can benefit from patents and copyright? In what ways it might be a challenge to work around. Please just explain how they work instead of personal opinion. Thanks a lot.

I'm currently working towards getting a chemistry minor, and one of my friends told me that her dad is a chemical engineer and has 4 patents that are quite lucrative for him. I know all too well that it's not as simple as walking into the lab and throwing chemicals together- a lot of research, hours of experimentation, and hardwork has to go into R&D for something to be considered successful. I also know that if you're working for a chemical company, they probably end up with the chemical patent. How can you be sure that you yourself would get the patent, how long do patents last, and do you think this would be a good idea to make money, or does the time investment outweigh the benefit?

Apparently oil companies will buy patents to alternative fuels and do nothing with them so no one can take advantage of these alternative fuels, hence forcing us to keep buying gas.